FYI:
In the current biocyc family of biopax.owl files, the following
property statements will cause "inconsistent" ontologies in SWOOP and
Protege4Alpha.
<bp:MOLECULAR-WEIGHT>18.015</bp:MOLECULAR-WEIGHT>
<bp:STOICHIOMETRIC-COEFFICIENT>1</bp:STOICHIOMETRIC-COEFFICIENT>
<bp:DELTA-G>0.4 </bp:DELTA-G>
In SWOOP this error message will read:
> Consistent: No
> Reason: Plain literal "18.015" does not belong to datatype http://> www.w3.org/2001/XMLSchema#double. Literal value may be missing the
> rdf:datatype attribute.
In Protege4Alpha an error message indicates that the ontology is
inconsistent, but no message yet as to why. However in the
individuals tab, the Value associated with the Property (MOLECULAR-
WEIGHT or STOICHIOMETRIC-COEFFICIENT or DELTA-G) indicates the error.
For example:
Property Value
bpx1:MOLECULAR-WEIGHT <Error! null>
To fix these, you can globally add the rdf:datatype property so the
statements look like this:
<bp:MOLECULAR-WEIGHT rdf:datatype="http://www.w3.org/2001/
XMLSchema#double">186.058</bp:MOLECULAR-WEIGHT>
<bp:STOICHIOMETRIC-COEFFICIENT rdf:datatype="http://www.w3.org/2001/
XMLSchema#double">1</bp:STOICHIOMETRIC-COEFFICIENT>
<bp:DELTA-G rdf:datatype="http://www.w3.org/2001/
XMLSchema#double">0.4 </bp:DELTA-G>
I did a global search and replace of
this with this
<bp:MOLECULAR-WEIGHT> <bp:MOLECULAR-WEIGHT
rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
<bp:STOICHIOMETRIC-COEFFICIENT> <bp:STOICHIOMETRIC-COEFFICIENT
rdf:datatype="http://www.w3.org/2001/XMLSchema#double">
<bp:DELTA-G> <bp:DELTA-G rdf:datatype="http://www.w3.org/
2001/XMLSchema#double">
Thanks to Bijan Parsia for help in tracking this down.